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Lisowiec-Wąchnicka J, Bartyś N, Pasternak A. A systematic study on the influence of thermodynamic asymmetry of 5'-ends of siRNA duplexes in relation to their silencing potency. Sci Rep 2019; 9:2477. [PMID: 30792489 PMCID: PMC6385221 DOI: 10.1038/s41598-018-36620-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 11/23/2018] [Indexed: 01/04/2023] Open
Abstract
siRNA molecules possess high potential as molecular tools and can be used as effective therapeutics in humans. One of the key steps in the action of these molecules is the choice of antisense strand by the RNA-induced silencing complex (RISC). To explain this process, we verified the theory which states that antisense strand selection is based on the thermodynamically less stable 5′ end of siRNA. Based on the studies presented herein, we observed that for the tested siRNA duplexes, the difference in the thermodynamic stability of the terminal, penultimate and pre-penultimate pairs in the duplex siRNA is not the dominant factor in antisense strand selection. We found that both strands in each tested siRNA molecule are used as an antisense strand. The introduction of modified nucleotides, whose impact on the thermodynamic stability of siRNA duplexes was studied, results in changes in antisense strand selection by the RISC complex. The presence of a modified residue often caused predominant selection of only one antisense strand which is at variance with the theory of siRNA strand bias.
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Affiliation(s)
- Jolanta Lisowiec-Wąchnicka
- Department of Nucleic Acids Bioengineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Natalia Bartyś
- Department of Nucleic Acids Bioengineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Anna Pasternak
- Department of Nucleic Acids Bioengineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.
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Wei J, Ouyang Y, Li X, Zhu B, Yang J, Cui Y, Chen X, Lin F, Long M, Yang A, Dong K, Zhang H. Early growth response gene 1, a TRBP binding protein, is involved in miRNA activity of miR-125a-3p in human cells. Cell Signal 2015; 27:1120-8. [PMID: 25725290 DOI: 10.1016/j.cellsig.2015.02.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 01/28/2015] [Accepted: 02/16/2015] [Indexed: 11/30/2022]
Abstract
BACKGROUND MicroRNAs (miRNAs) are key regulators of many cellular pathways. However, the picture for components or regulators involved in the process of miRNA biogenesis and function remains to be further elucidated. Early growth response gene 1 (Egr1) has long been considered as tumor suppressor and transcriptional factor involved in cell proliferation and regulation of apoptosis. RESULTS Here we show that Egr1 is able to modulate guide strand loading of certain miRNAs or siRNAs in human HEK293 and A549 cells, which is related with thermodynamic parameters of miRNA or siRNA. Further, we found that Egr1 modulates the silencing activity of miR-125a-3p in vivo. Immunoprecipitation experiment demonstrated that Egr1 could bind miRNA biogenesis protein TAR RNA-binding protein2 (TRBP2), and knockdown TRBP by RNAi abolished the regulating effects of Egr1 on miR-125a-3p efficiency. Further experiments revealed that deleting sequence 97-227aa containing dsRBD B domain of TRBP eliminated the binding phenomenon between Egr1 and TRBP and impaired the effect of Egr1 on miR-125a-3p efficiency. CONCLUSIONS Taken together, our study has demonstrated that Egr1 is able to regulate miRNA activity of miR-125a-3p in human cells through binding TRBP, which highlights an unexpected function of Egr1 in miRNA pathway.
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Affiliation(s)
- Junxia Wei
- Department of Clinical Laboratory and Research Center, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Yongri Ouyang
- Department of Clinical Laboratory and Research Center, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Xia Li
- Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, China
| | - Baoyi Zhu
- Department of Ophthalmology, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Jie Yang
- Department of Nephroloogy, Tangdu Hospital, The Fourth Military Medical University, Xi'an, China
| | - Ying Cui
- Department of Clinical Laboratory and Research Center, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Xi Chen
- Department of Clinical Laboratory and Research Center, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Fang Lin
- Department of Clinical Laboratory and Research Center, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Min Long
- Department of Clinical Laboratory and Research Center, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Angang Yang
- Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, China
| | - Ke Dong
- Department of Clinical Laboratory and Research Center, Tangdu Hospital, Fourth Military Medical University, Xi'an, China.
| | - Huizhong Zhang
- Department of Clinical Laboratory and Research Center, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
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Zheng J, Zhang L, Zhang J, Wang X, Ye K, Xi Z, Du Q, Liang Z. Single modification at position 14 of siRNA strand abolishes its gene-silencing activity by decreasing both RISC loading and target degradation. FASEB J 2013; 27:4017-26. [PMID: 23771927 DOI: 10.1096/fj.13-228668] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Normally siRNA has to be chemically stabilized in therapeutic applications. It is a challenge to obtain optimal stabilizing effects while maintaining full silencing activity due to a lack of understanding of how different chemical modifications would influence the efficacy of siRNA. In the current study, the effect of single 2'-sugar modifications was profiled across the length of the siRNA guide strand. This led to the surprising finding that a single 2'-OMe modification at position 14 of the siRNA guide strand substantially compromised its gene-silencing activity in a manner that was independent of the nucleotide identity at this site or the sequence context around it. We found that modification at position 14 of the siRNA guide strand reduced its RNA-induced silencing complex (RISC) loading tremendously, whereas the loading of the siRNA sense strand was only marginally affected. When comparing the silencing potency of 14th position-modified siRNA (transfected at 16.7 nM) and native control (transfected at 1 nM) at equivalent Ago2 loading levels, the silencing potency of modified siRNA was much lower, even lower than the level of native siRNA transfected at 0.1 nM. These data indicated that modification at position 14 of the siRNA guide strand abolishes its gene-silencing activity by decreasing both RISC loading and target degradation. Using a computational modeling approach, we demonstrated an intimate interaction between the 14th nucleotide of guide strand and the amino acid Q675 in the AGO protein, which is located in a highly conserved loop of PIWI domain. In addition to gaining insights into siRNA-AGO interactions, this study of structure-activity relationship further established a general principle for siRNA modification in siRNA drug development.
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Affiliation(s)
- Jie Zheng
- 1Z.L., Institute of Molecular Medicine, Peking University, Beijing, 100871, China.
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4
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Wu H, Ma H, Ye C, Ramirez D, Chen S, Montoya J, Shankar P, Wang XA, Manjunath N. Improved siRNA/shRNA functionality by mismatched duplex. PLoS One 2011; 6:e28580. [PMID: 22174840 PMCID: PMC3235145 DOI: 10.1371/journal.pone.0028580] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Accepted: 11/10/2011] [Indexed: 11/26/2022] Open
Abstract
siRNA (small interfering RNA) and shRNA (small hairpin RNA) are powerful and commonly used tools in biomedical research. Currently, siRNAs are generally designed as two 21 nt strands of RNA that include a 19 nt completely complementary part and a 2 nt overhang. However, since the si/shRNAs use the endogenous miRNA machinery for gene silencing and the miRNAs are generally 22 nt in length and contain multiple internal mismatches, we tested if the functionality can be increased by designing the si/shRNAs to mimic a miRNA structure. We systematically investigated the effect of single or multiple mismatches introduced in the passenger strand at different positions on siRNA functionality. Mismatches at certain positions could significantly increase the functionality of siRNAs and also, in some cases decreased the unwanted passenger strand functionality. The same strategy could also be used to design shRNAs. Finally, we showed that both si and miRNA structured oligos (siRNA with or without mismatches in the passenger strand) can repress targets in all individual Ago containing cells, suggesting that the Ago proteins do not differentiate between si/miRNA-based structure for silencing activity.
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Affiliation(s)
- Haoquan Wu
- Center of Excellence in Infectious Disease Research, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas, United States of America
- * E-mail: (HW); (NM)
| | - Hongming Ma
- Center of Excellence in Infectious Disease Research, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas, United States of America
| | - Chunting Ye
- Center of Excellence in Infectious Disease Research, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas, United States of America
| | - Danielle Ramirez
- Center of Excellence in Infectious Disease Research, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas, United States of America
| | - Shuiping Chen
- Center of Excellence in Infectious Disease Research, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas, United States of America
| | - Jessica Montoya
- Center of Excellence in Infectious Disease Research, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas, United States of America
| | - Premlata Shankar
- Center of Excellence in Infectious Disease Research, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas, United States of America
| | - Xiaozhong A. Wang
- Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, Evanston, Illinois, United States of America
| | - N. Manjunath
- Center of Excellence in Infectious Disease Research, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas, United States of America
- * E-mail: (HW); (NM)
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Kini HK, Walton SP. Effect of siRNA terminal mismatches on TRBP and Dicer binding and silencing efficacy. FEBS J 2009; 276:6576-85. [PMID: 19811537 DOI: 10.1111/j.1742-4658.2009.07364.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To enhance silencing and avoid off-target effects, siRNAs are often designed with an intentional bias to ensure that the end of the siRNA that contains the guide strand 5' end is less stably hybridized relative to the end containing the passenger strand 5' end. One means by which this is accomplished is to introduce a terminal mismatch, typically by changing the passenger strand sequence to impair its hybridization with the guide strand 5' end. However, there are conflicting reports about the influence of terminal mismatches on the silencing efficacy of siRNAs. Here, the silencing efficiency of siRNAs with a terminal mismatch generated either by altering the guide strand (at the 5' end, nucleotide 1) or the passenger strand (nucleotide 19 from the 5' end) was examined. Subsequently, we studied the relationship between the silencing efficiency of the siRNAs and their binding to the RNA-induced silencing complex loading complex proteins HIV transactivating response RNA-binding protein and Dicer in H1299 cytoplasmic extracts. Binding of siRNA and the transactivating response RNA-binding protein was significantly reduced by terminal mismatches, which largely agrees with the reduction in eventual silencing efficacy of the siRNAs. Single terminal mismatches led to a small increase in Dicer binding, as expected, but this did not lead to an improvement in silencing activity. These results demonstrate that introduction of mismatches to control siRNA asymmetry may not always improve target silencing, and that care should be taken when designing siRNAs using this technique.
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Affiliation(s)
- Hemant K Kini
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824-1226, USA
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Xu N, Gkountela S, Saeed K, Akusjärvi G. The 5'-end heterogeneity of adenovirus virus-associated RNAI contributes to the asymmetric guide strand incorporation into the RNA-induced silencing complex. Nucleic Acids Res 2009; 37:6950-9. [PMID: 19755500 PMCID: PMC2777419 DOI: 10.1093/nar/gkp764] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Human Adenovirus type 5 encodes two short RNA polymerase III transcripts, the virus-associated (VA) RNAI and VA RNAII, which can adopt stable hairpin structures that resemble micro-RNA precursors. The terminal stems of the VA RNAs are processed into small RNAs (mivaRNAs) that are incorporated into RISC. It has been reported that VA RNAI has two transcription initiation sites, which produce two VA RNAI species; a major species, VA RNAI(G), which accounts for 75% of the VA RNAI pool, and a minor species, VA RNAI(A), which initiates transcription three nucleotides upstream compared to VA RNAI(G). We show that this 5′-heterogeneity results in a dramatic difference in RISC assembly. Thus, both VA RNAI(G) and VA RNAI(A) are processed by Dicer at the same position in the terminal stem generating the same 3′-strand mivaRNA. This mivaRNA is incorporated into RISC with 200-fold higher efficiency compared to the 5′-strand of mivaRNAI. Of the small number of 5′-strands used in RISC assembly only VA RNAI(A) generated active RISC complexes. We also show that the 3′-strand of mivaRNAI, although being the preferred substrate for RISC assembly, generates unstable RISC complexes with a low in vitro cleavage activity, only around 2% compared to RISC assembled on the VA RNAI(A) 5′-strand.
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Affiliation(s)
- Ning Xu
- Department of Medical Biochemistry and Microbiology, Uppsala Biomedical Center, Husargatan 3, S-751 23 Uppsala, Sweden
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Wei JX, Yang J, Sun JF, Jia LT, Zhang Y, Zhang HZ, Li X, Meng YL, Yao LB, Yang AG. Both strands of siRNA have potential to guide posttranscriptional gene silencing in mammalian cells. PLoS One 2009; 4:e5382. [PMID: 19401777 PMCID: PMC2671169 DOI: 10.1371/journal.pone.0005382] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Accepted: 03/27/2009] [Indexed: 11/19/2022] Open
Abstract
Despite the widespread application of RNA interference (RNAi) as a research tool for diverse purposes, the key step of strand selection of siRNAs during the formation of RNA-induced silencing complex (RISC) remains poorly understood. Here, using siRNAs targeted to the complementary region of Survivin and the effector protease receptor 1 (EPR-1), we show that both strands of the siRNA duplex can find their target mRNA and are equally eligible for assembly into Argonaute 2 (Ago2) of RISC in HEK293 cells. Transfection of the synthetic siRNA duplexes with different thermodynamic profiles or short hairpin RNA (shRNA) vectors that generate double-stranded RNAs (dsRNAs), permitting processing specifically from either the 5' or 3' end of the incipient siRNA, results in the degradation of the respective target mRNAs of either strand of the siRNA duplex with comparable efficiencies. Thus, while most RNAi reactions may follow the thermodynamic asymmetry rule in strand selection, our study suggests an exceptional mode for certain siRNAs in which both strands of the duplex are competent in sponsoring RNAi, and implies additional factors that might dictate the RNAi targets.
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MESH Headings
- Argonaute Proteins
- Base Sequence
- Carboxypeptidases/metabolism
- Cell Line
- Cytidine/analogs & derivatives
- DNA Primers/genetics
- Eukaryotic Initiation Factor-2/metabolism
- Humans
- Inhibitor of Apoptosis Proteins
- Microtubule-Associated Proteins/antagonists & inhibitors
- Microtubule-Associated Proteins/genetics
- RNA Interference
- RNA Processing, Post-Transcriptional
- RNA, Complementary/chemistry
- RNA, Complementary/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Small Interfering/chemistry
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- Receptors, Cell Surface/antagonists & inhibitors
- Receptors, Cell Surface/genetics
- Ribonuclease III/metabolism
- Survivin
- Thermodynamics
- Uridine/analogs & derivatives
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Affiliation(s)
- Jun-Xia Wei
- State Key Laboratory of Cancer Biology; Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, China
- Department of Clinical Diagnosis, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Jie Yang
- State Key Laboratory of Cancer Biology; Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, China
- Department of Nephrology, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Ji-Feng Sun
- Department of Nephrology, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Lin-Tao Jia
- State Key Laboratory of Cancer Biology; Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, China
| | - Yong Zhang
- Department of Immunology, Fourth Military Medical University, Xi'an, China
| | - Hui-Zhong Zhang
- Department of Clinical Diagnosis, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Xia Li
- State Key Laboratory of Cancer Biology; Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, China
| | - Yan-Ling Meng
- Department of Immunology, Fourth Military Medical University, Xi'an, China
| | - Li-Bo Yao
- State Key Laboratory of Cancer Biology; Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, China
| | - An-Gang Yang
- State Key Laboratory of Cancer Biology; Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, China
- Department of Immunology, Fourth Military Medical University, Xi'an, China
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Abstract
An efficient mechanism for the sequence‐specific inhibition of gene expression is RNA interference. In this process, double‐stranded RNA molecules induce cleavage of a selected target RNA (see picture). This technique has in recent years developed into a standard method of molecular biology. Successful applications in animal models have already led to the initiation of RNAi‐based clinical trials as a new therapeutic option.WILEY-VCH Only ten years ago Andrew Fire and Craig Mello were able to show that double‐stranded RNA molecules could inhibit the expression of homologous genes in eukaryotes. This process, termed RNA interference, has developed into a standard method of molecular biology. This Review provides an overview of the molecular processes involved, with a particular focus on the posttranscriptional inhibition of gene expression in mammalian cells, the possible applications in research, and the results of the first clinical studies.
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Affiliation(s)
- Jens Kurreck
- Institute of Industrial Genetics, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany.
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Affiliation(s)
- Jens Kurreck
- Institut für Industrielle Genetik, Universität Stuttgart, Allmandring 31, 70569 Stuttgart (Deutschland), Fax: (+49) 711‐685 66973 http://www.uni‐stuttgart.de/iig/institut/staff/kurreck/index.html
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